A new blueprint for the hidden world beneath San Francisco Bay’s shimmering waters calls for thousands of acres of oyster beds and eelgrass, beach replenishment projects and research.

The report, a four-year study by state and federal agencies, is a follow-up to an influential 1999 blueprint that paved the way for a major acceleration of wetlands restoration around the bay, now the largest wetlands restoration program on the West Coast.

Thursday’s Subtidal Habitat report is less specific than the earlier Baylands Habitat Goals report because less is known about the ecosystem hidden underwater.

But researchers hope it paves the way for more study and restoration projects over the next 50 years, leading to a healthier bay for bottom-dwelling organisms and for the salmon, herring, shorebirds, pelicans and sea lions that ride higher on the same food chain.

It contains no cost estimate, mostly because many of the initiatives have not been tried on a large scale. The report suggests trying small projects, such as oyster bed restoration and pilings removal before moving on to larger projects.

No one knows the extent of the bay’s oyster beds, mostly because the water’s murkiness makes it difficult to see exactly where they are and how far they spread.

But the bay’s native Olympia oysters continue to survive and the bay has several hundred thousand tons of fossilized oyster shells, said Marilyn Latta, project manager for the report at the State Coastal Conservancy.

The report calls for expanding oyster beds to 8,000 acres, nearly half of which could be off Contra Costa’s shore between Point San Pablo and Point Pinole.

Could that support commercial oyster farming?

“That would be a great dream far off in the future,” said Latta. “It is not at all related to our planning now, though. It would not be healthy for people to eat them now.”

Because they are filter-feeders, oysters would absorb too many pollutants, including mercury, selenium, hydrocarbons, PCBs, pharmaceuticals and other toxic materials, Latta said.

The report also calls for tripling the area of the bay’s eelgrass beds from 4,000 acres to 12,000 acres.

More eelgrass would mean more places for herring, for example, to lay eggs. The biggest eelgrass bed containing more than one-third of the bay’s growth is near Richmond.

“It forms these meadows that do a lot of beneficial things for the bay,” Latta said.

The report suggests creating eelgrass reserves but does not say what kinds of restrictions might be needed to protect them from damage by boats, construction or dredging. Latta said it was beyond the report’s scope to recommend specific eelgrass reserves.

Some of the areas suggested include Point San Pablo, Crown Beach, Richardson Bay and Coyote Point.

The report also suggests using clean sand from maintenance dredging to build up beaches at Eastshore State Park, Point Isabella Regional Shoreline, San Rafael Shoreline and others.

As a result of the 1999 wetlands report, the amount of wetlands, or baylands, ringing San Francisco Bay has increased. There were about 40,000 acres of wetlands at the time of the report, and nearly that much has either been restored or is on the way to being restored. The earlier report set a goal of 100,000 acres total acres.

“The acquisition and protection of shoreline properties has been greatly advanced by the publishing of the habitat goals report because it brought a strong scientific consensus of needs and how to do it,” said David Lewis, executive director of Save the Bay, an environmental group.

A third report on the Bay Area’s upland habitat, which will include the nine Bay Area counties, is nearing completion, Latta said.

The report released Thursday, San Francisco Bay Subtidal Habitat Goals Report, was developed by the State Coastal Conservancy, the National Marine Fisheries Service, the San Francisco Bay Conservation and Development Commission and the San Francisco Estuary Partnership. It was expected to be available Thursday at www.sfbaysubtidal.org.

Researchers said Sunday the mass die-off occurred because unusually large amounts of sea ice forced penguin parents to travel farther in search of food for their young. By the time they returned, only two out of thousands of chicks had survived.